Dear Amber developers and users,
I'm using antechamber to compute bcc charges for several ligands. I've
run the same simulation using ambertools15 and ambertools17, using
either mopac (MOPAC2016.exe, version: 16.230L, under Ubuntu 16.04) or
sqm. I noticed that, while sqm bcc charges were consistent among the two
AmberTools versions, those computed by mopac were subtantially
different. Summing the total charges computed with different methods I
obtained:
AT15/sqm: 0.002001
AT15/mopac: -0.000002
AT17/sqm: 0.002001
AT17/mopac: 0.064285
The script I use to launch mopac has been modified as follow:
export LD_LIBRARY_PATH=/opt/mopac:$LD_LIBRARY_PATH
cp mopac.in mopac.in.orig
sed -i 's/ANALYT //g' mopac.in
ln -s mopac.in mopac
/opt/mopac/MOPAC2016.exe mopac
rm mopac
I noticed that the mopac.in files for AT15/mopac and AT17/mopac differed
for a blank line between title and coordinates. I've tried to insert the
blank line back, by modifying the mopac.sh script, and the problem was
fixed:
export LD_LIBRARY_PATH=/opt/mopac:$LD_LIBRARY_PATH
cp mopac.in mopac.in.orig
sed -i 's/ANALYT //g' mopac.in
sed -i '/created by wmopcrt/G' mopac.in
ln -s mopac.in mopac
/opt/mopac/MOPAC2016.exe mopac
rm mopac
All the files/logs necessary to reproduce those results are included in
the .tgz here attached.
Please let me know if this issue is going to be solved in future
release, in order to avoid parameterization of hundreds of ligands with
double spacing ;-)
Best,
Alessandro
--
Alessandro Contini, PhD
Dipartimento di Scienze Farmaceutiche
Sezione di Chimica Generale e Organica "A. Marchesini"
Via Venezian, 21 20133 Milano
tel. +390250314480
e-mail alessandro.contini.unimi.it
skype alessandrocontini
http://www.scopus.com/authid/detail.url?authorId=7003441091
http://orcid.org/0000-0002-4394-8956
http://www.researcherid.com/rid/F-5064-2012
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Received on Wed Jun 21 2017 - 05:00:03 PDT
